VSDMIP: virtual screening data management on an integrated platform.
A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.
Gil-Redondo
Rubén
R
Unidad De Bioinformática, Centro De Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera 1, Campus De Cantoblanco, Madrid 28049, Spain.
Estrada
Jorge
J
Morreale
Antonio
A
Herranz
Fernando
F
Sancho
Javier
J
Ortiz
Angel R
AR
D003628:Database Management Systems; D030562:Databases, Protein; D015195:Drug Design; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D054852:Small Molecule Libraries; D012997:Solvents / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D054852:Small Molecule Libraries; D012997:Solvents